PDB entry 4mby

View 4mby on RCSB PDB site
Description: Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactose
Class: viral protein
Keywords: jelly roll, Polyomavirus, viral capsid (structural) protein, DNA encapsidation, receptor binding, Sialylated oligosaccharides, VIRAL PROTEIN
Deposited on 2013-08-21, released 2013-12-04
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-01-22, with a file datestamp of 2014-01-17.
Experiment type: XRAY
Resolution: 1.48 Å
R-factor: 0.166
AEROSPACI score: 0.57 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY (Start-277)
    Domains in SCOPe 2.07: d4mbya_
  • Chain 'B':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyb_
  • Chain 'C':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyc_
  • Chain 'D':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyd_
  • Chain 'E':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY (Start-277)
    Domains in SCOPe 2.07: d4mbye_
  • Chain 'F':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyf_
  • Chain 'G':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyg_
  • Chain 'H':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyh_
  • Chain 'I':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyi_
  • Chain 'J':
    Compound: Major capsid protein VP1
    Species: B-lymphotropic polyomavirus [TaxId:332091]
    Gene: VP1
    Database cross-references and differences (RAF-indexed):
    • PDB 4MBY
    Domains in SCOPe 2.07: d4mbyj_
  • Heterogens: CA, CL, EDO, IPA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4mbyA (A:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyA (A:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4mbyB (B:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyB (B:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivknp
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4mbyC (C:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyC (C:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivknp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4mbyD (D:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyD (D:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtctilmweavsvktevvgisslvnlhqggkyiygsssgcvpv
    qgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgkyp
    vevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsca
    diagvhtnysetqvwrglpryfnvtlrkrivknp
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4mbyE (E:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyE (E:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4mbyF (F:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyF (F:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivkn
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4mbyG (G:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyG (G:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnmtctilmweavsvktevvgisslvnlhqggkyiygsssgcvpvqg
    ttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgkypve
    vwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflscadi
    agvhtnysetqvwrglpryfnvtlrkrivk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4mbyH (H:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyH (H:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtctilmweavsvktevvgisslvnlhqggkyiygsssgcvpv
    qgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgkyp
    vevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsca
    diagvhtnysetqvwrglpryfnvtlrkrivkn
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >4mbyI (I:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyI (I:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvpv
    qgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgkyp
    vevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsca
    diagvhtnysetqvwrglpryfnvtlrkrivkn
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >4mbyJ (J:)
    gshmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkd
    tlpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcv
    pvqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgk
    ypvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklfls
    cadiagvhtnysetqvwrglpryfnvtlrkrivknpyp
    

    Sequence, based on observed residues (ATOM records): (download)
    >4mbyJ (J:)
    shmggvevlevrtgpdaitqieaylnprmgnnipsedlygysnsintafskasdtpnkdt
    lpcysvaviklpllnedmtcdtilmweavsvktevvgisslvnlhqggkyiygsssgcvp
    vqgttyhmfavggeplelqglvasstatypddvvaiknmkpgnqgldpkakalldkdgky
    pvevwcpdpsknentryygsftggattppvmqftnsvttvlldengvgplckgdklflsc
    adiagvhtnysetqvwrglpryfnvtlrkrivknp